Flavivirus NS5A proteins for the treatment of HIV

ABSTRACT

GB virus C (GBV-C or hepatitis G virus) is a flavivirus that frequently leads to chronic viremia in humans. The invention provides compositions and methods involving a-GBV-C NS5A peptide or polypeptide for inhibiting and treating HIV infections.

BACKGROUND OF THE INVENTION

The present application claims benefit of priority to U.S. Provisional Application Ser. No. 60/653,823, filed Feb. 17, 2005, the entire contents of which are hereby incorporated by reference.

The U.S. Government own rights in this invention pursuant to grant number A158740 from NIH and merit grants awarded to Jack Stapleton and Jinhua Xiang from the Veterans Administration.

I. Field of the Invention

The present invention relates generally to the fields of molecular biology and virology. More particularly, it concerns methods and compositions to treat, inhibit or prevent HIV infection.

II. Description of Related Art

A. GB Virus Type C

GB virus type C (GBV-C), also known as hepatitis G virus (HGV), is a virus whose genomic organization and nucleotide sequence places it in the Flavivirus family (Robertson et al., 1998). It is the most closely related human virus to hepatitis C virus (HCV) (Leary et al., 1996; Linnen et al., 1996; Simons et al., 1995). It has been suggested that these viruses should be classified together with non-human GB-hepatitis agents as the hepacivirus genus. Although GBV-C was originally associated with post-transfusion hepatitis in humans (Linnen et al., 1996), subsequent epidemiological studies indicated that it does not cause acute or chronic hepatitis (Alter et al., 1997a; Alter et al., 1997b). In addition, experimental GBV-C infection of chimpanzees was not associated with acute hepatitis (Bukh et al., 1998).

Persistent GBV-C viremia (as detected by RT-PCR) is common, with 0.9% to 3% of healthy U.S. blood donors and approximately 20%-30% of patients with HCV infection persistently infected with GBV-C (Dawson et al., 1996; Feucht et al., 1997; Simons et al., 1995a; Simons et al., 1995b; Tacke et al., 1997). Following infection, about 80% of people clear their viremia, concomitantly developing antibody to the GBV-C E2 protein (Feucht et al., 1997; Thomas et al., 1998). Thus, it is estimated that approximately 20% of infected people remain viremic for long periods of time. GBV-C appears to be transmitted primarily by parenteral exposure (Simons et al., 1995), although there are data suggesting that sexual and/or household transmission of GBV-C infection may occur (Akiyoshi et al., 1999; de Martino et al., 1998; Nerurkar et al., 1998; Tanaka et al., 1997; Wu et al., 1997).

B. GBV-C and HIV

During progressive human immunodeficiency virus type 1 (HIV-1) infection, the virus-specific immune responses of an infected subject gradually deteriorate, leading to the development of acquired immunodeficiency syndrome (AIDS). Most infected patients do not exhibit overt clinical manifestations of the disease for six to ten years following initial infection, however, most individuals infected with HIV eventually die from conditions or infections; that the individual's immune system is no longer equipped to fight. While treatment for AIDS has been forthcoming, no effective cure has been reported. Thus, preventative and treatment options against HIV infection and the development of AIDS remain highly desirable.

GBV-C has been investigated in the context of HIV infection. The course of HIV-1 infection is extremely variable among infected individuals, although the reasons for this observation are not fully understood. Individuals whose HIV disease progresses slowly are often called long-term non-progressors (LTNPs). The prevalence of LTNPs varies from 1% to 25% of infected people, depending upon the definition used (reviewed in Easterbrook, 1999). There are no specific clinical criteria for LTNP. However, non-progression generally implies the absence of HIV-related clinical disease 10 or more years following infection and an absolute CD4 count of ≧500 cells/mm³ (Easterbrook, 1999). Evaluation of LTNP's has identified HIV isolates with deletions in key replicative genes (Deacon et al., 1995) and host genetic factors, including specific HLA haplotypes (reviewed in reference Rowland-Jones, 1999). In some individuals, polymorphisms that result in absent or reduced expression of HIV co-receptors have been identified (Huang et al., 1996). However, these findings are uncommon and thought to account for no more than one-third of LTNP's (Rowland-Jones, 1999).

Persistent GBV-C infection is common in humans, with infection rates of approximately 0.9% to 3% in healthy blood donors, 20-30% in HCV-positive people (Dawson et al., 1996), and 35%-40% in HIV-positive individuals. GBV-C infection can persist for decades in the absence of any clinical morbidity or mortality. Among immune-competent individuals, it is estimated that 60% to 75% of GBV-C-infected people clear the infection, concomitantly developing antibodies to the envelope glycoprotein E2 (Thomas et al., 1998). It is also known that GBV-C can be propagated in cultures of peripheral blood mononuclear cells (PBMC's) (Fogeda et al., 1999).

In 1998, Toyoda et al. found that hemophiliacs co-infected with HIV and GBV-C had a lower plasma HIV RNA concentration and a lower incidence of AIDS diagnoses compared to those infected with HIV alone (Toyoda et al., 1998), although the differences were not statistically significant. In contrast, Sabin and colleagues found an increased rate of AIDS and death in hemophiliacs “exposed” to GBV-C (Sabin et al., 1998) compared to non-exposed individuals. This study included HIV-positive subjects who were either GBV-C viremic as determined by detection of GBV-C RNA in plasma, or HIV-infected people who were not viremic but were anti-GBV-C E2 antibody-positive. Although the mortality rate was higher among the GBV-C “exposed” individuals, the results were not statistically significant. Looking at HIV-infected persons, Lefrere and colleagues reported a significant delay in the rate of CD4+ T cell decline, development of AIDS, and death in 23 HIV-positive individuals with GBV-C viremia compared to 72 HIV-infected people without GBV-C viremia (Lefrère et al., 1999). In that study, HIV-infected individuals who were also GBV-C-positive were compared to HIV-infected individuals who were GBV-C-negative. When these subjects were matched by age, sex, baseline HIV RNA load, and baseline CD4 T cell count, HIV disease progression appeared to be worse in GBV-C-negative subjects.

The interrelationship between HIV and GBV-C continues to be explored, with possible therapeutic aspects of GBV-C infection being examined.

SUMMARY OF THE INVENTION

A pharmaceutical composition comprising an isolated flavivirus NS5A peptide or polypeptide, or multiple flavivirus NS5A peptides from the same or different NS5A polypeptide. The NS5A polypeptide may be a full length NS5A polypeptide, a fusion polypeptide. The fusion may comprise a targeting signal, such as a nuclear targeting signal or a cell surface receptor (e.g., a CD4 receptor). The NS5A peptide or polypeptide may be formulated in a lipid vehicle, such a liposome. The NS5A peptide or polypeptide may be formulated with an amphipathic peptide, an insect peptide, or pyrrhocoricin. The flavivirus may be selected from the group consisting of DEN4, YFV, TBEV, WNV, CSFV, BVDV, GBV-A, GBV-B, GBV-C, HGV, HCV2a, HCV3a, HCV2b, HCV1a and HCV1b. The flavivirus NS5A peptide or polypeptide may residues 152-237 of GBV-C NS5A, or the corresponding sequences thereto from other flavivirus NS5A proteins, or may comprise domain II of HCV NS5A, or the corresponding sequences thereto from other flavivirus NS5A proteins. The NS5A peptide or polypeptide may be from a IFN-sensitive flavivirus, or a IFN-resistant flavivirus. The IFN-sensitive flavivirus or IFN-resistant flavivirus may be a GBV-C virus.

In yet another embodiment, there is provided a method for preventing or treating HIV infection comprising administering to a subject a composition comprising a flavivirus NS5A peptide or polypeptide. The flavivirus NS5A peptide or polypeptide comprises multiple flavivirus NS5A peptides, from the same or different NS5A polypeptides. The NS5A polypeptide may be a full length NS5A polypeptide, and may be a fusion polypeptide, for example, comprising a targeting signal, such as a nuclear targeting signal or a targeting signal that targets a cell surface receptor (e.g., the CD4 receptor). The NS5A peptide or polypeptide may be formulated in a lipid vehicle, such a liposome. The NS5A peptide or polypeptide may be formulated with an amphipathic peptide, an insect peptide, or pyrrhocoricin. The flavivirus may be selected from the group consisting of DEN4, YFV, TBEV, WNV, CSFV, BVDV, GBV-A, GBV-B, GBV-C, HGV, HCV2a, HCV3a, HCV2b, HCV1a and HCV1b. The flavivirus NS5A peptide or polypeptide may residues 152-237 of GBV-C NS5A, or the corresponding sequences thereto from other flavivirus NS5A proteins, or may comprise domain II of HCV NS5A, or the corresponding sequences thereto from other flavivirus NS5A proteins. The NS5A peptide or polypeptide may be from a IFN-sensitive flavivirus, or a IFN-resistant flavivirus. The IFN-sensitive flavivirus or IFN-resistant flavivirus may be a GBV-C virus. The method may further comprise administration of at least a second anti-HIV therapy, before or after said flavivirus NS5A peptide or polypeptide. The second anti-HIV therapy may be HAART therapy, or AZT therapy. The method may comprise multiple administrations of the composition.

In yet another embodiment, there is provided a method of reducing HIV replication in an HIV-infected cell comprising contacting said cell with a composition comprising a flavivirus NS5A peptide or polypeptide. The cell may be a T lymphocyte. In still yet another embodiment, there is provided a method of inhibiting HIV infection of a cell comprising contacting said cell with a composition comprising a flavivirus NS5A peptide or polypeptide. The cell may be a T lymphocyte.

In still a further embodiment, there is provided a method for preventing or treating HIV infection comprising administering to a subject a composition comprising an expression construct encoding a flavivirus NS5A peptide or polypeptide. The expression construct may be a viral expression construct, such as an adenovirus, a retrovirus, a lentivirus, an adeno-associated virus, a polyoma virus, a herpesvirus, or a pox virus. The expression construct may be a non-viral expression construct, for example, dispersed in a lipid vehicle. The expression construct may encode an NS5A polypeptide or an NS5A peptide, a a full length NS5A polypeptide, a fusion polypeptide, for example, comprising a nuclear targeting signal or a signal that targets a cell surface receptor, e.g., the CD4 receptor. The flavivirus NS5A peptide or polypeptide may comprise residues 152-237 of GBV-C NS5A, or the corresponding sequences thereto from other flavivirus NS5A proteins, or domain II of HCV NS5A, or the corresponding sequences thereto from other flavivirus NS5A proteins. The flavivirus may be selected from the group consisting of DEN4, YFV, TBEV, WNV, CSFV, BVDV, GBV-A, GBV-B, GBV-C, HGV, HCV2a, HCV3a, HCV2b, HCV1a and HCV1b.

The use of the word “a” or “an” when used in conjunction with the term “comprising” in the claims and/or the specification may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one.” Furthermore, where multiple steps of a method of process are cited, it is understood that the steps are not required to be performed in the particular order recited unless one of skill in the art is not be able to practice the method in a different order.

Other objects, features, and advantages of the present invention will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating preferred embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present invention. The invention may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein.

FIG. 1—NS5A expression in Jurkat cells. Jurkat cells containing GBV-C NS5A (A11a clone) expressed two immunoreactive proteins when incubated without doxycycline (Doxy). Rabbit anti-NS5A antisera was raised against NS5A expressed in E. Coli. This antigen is shown as the positive control on lower panel (+), whereas the positive control [C(+)] top panel represents NS5A expressed in CHO cells; JICR In Press). Growth of cells in low levels of doxycycline for 48 hrs reduced NS5A protein levels to non-detectable levels. Doxy concentration in mg/mi.

FIGS. 2A-C—HIV replication in Jurkat cells with and without NS5A expression. The amount of HIV p24 antigen released into culture supernatants from two cloned Jurkat cell lines expressing GBV-C NS5A (A11a and A11b) or vector control cell line (VC) 2 to 6 days following infection using an X-4 virus isolate (MOI of 0.1 (FIG. 2A) or 0.5 (FIG. 2B)). Cells were grown without doxycycline, and data represent the mean of 3 replicate samples. NS5A expression is shown (immunoblot of cell lysates in triplicate) of A11a, A11b. VC=vector control cell lysate. Note that A11a has greater levels of NS5A expressed and HIV replication in these cells is lower than in A11b (on day 6). Compared to vector control cells, HIV inhibition was significantly lower on day 6 (p=0.02).

FIG. 3A—Experimental Design. Jurkat cells with either vector control (VC) or NS5A were grown without doxycycline. Cells were divided, and half were maintained without doxycycline (NS5A was expressed) or with various doses of doxycycline (NS5A expression was differentially suppressed). Cells (VC and NS5A containing) were infected with X4 HIV-1 (clinical isolate) 48 hrs after dividing cells, and cell culture supernatants monitored 2, 4, and 6 days later for HIV p24 antigen.

FIG. 3B—Dose-dependent inhibition of HIV by NS5A. Experimental design described above. NS5A expression was suppressed by cell growth in various concentrations of doxycycline (0.01, 0.1 and 1 mg/ml as indicated) for 2 days prior to infection with HIV-1. HIV replication was monitored by measuring p24 antigen in culture supernatants. The amount of NS5A expression was directly correlated with inhibition of HIV expression in Jurkat-NS5A cells (left panel), and doxycycline had no effect in Jurkat-vector control cells (VC; right panel).

FIG. 4A—Experimental Design. Jurkat cells with NS5A were passaged with doxycycline to suppress NS5A expression. Cells were divided, and half were maintained without doxycycline (NS5A was expressed) or with 1 mg/ml doxycycline (NS5A was not expressed). NS5A containing cells were infected with X4 HIV-1 (clinical isolate) 96 hrs after cells were divided, and cell culture supernatants monitored 2, 4, and 6 days later for HIV p24 antigen.

FIG. 4B—GBV-C NS5A inhibits HIV replication. Data represent HIV replication (p24 antigen in supernatants). HIV replication was not different on days 1 and 2; however, by day 3, Jurkat-NS5A cells had 45% reduction in HIV p24 Ag 3 days post-infection (T-test, P=0.03), and by 56%-60% on days 4, 5, and 6 (p<0.001 for each day). Infections were performed in triplicate, NS5A and vector control error bars shown. Results were similar for Jurkat cells without any plasmid DNA as well.

FIG. 5—Release of SDF-1 into culture supernatants by Jurkat cells with or without GBV-C NS5A. SDF-1 in supernatants was measured by ELISA in triplicate at time points shown. There were no differences between Jurkat and vector control Jurkat cells; however, SDF-1 increased in NS5A expressing cells on days 5 and 6 (T test, P<0.001 for both days).

FIG. 6—Jurkat cells expressing GBV-C NS5A have lower surface density of CXCR4 compared to Jurkat cells with a vector control. Jurkat cells that express NS5A or the vector control were grown without doxycycline, and analyzed by flow cytometry for surface expression of CXCR4 (shown above). Reproducibly, cells with NS5A demonstrated a 49.6% reduction in CXCR4 mean fluorescence (p=0.003). No difference in CCR5 or CD4 was observed (data not shown). Preliminary microarray data demonstrated decreased levels of CXCR4 25 mRNA in NS5A expressing cells.

FIG. 7—Release of caspase 3/7 into culture supernants following incubation with anti-Fas antibody (CH11). Jurkat cells with NS5A were relatively resistant to induction of apoptosis by CH11 when compared to Jurkat cells with the vector control. Similarly, spontaneous apoptosis was greater in Jurkat NS5A cells compared to vector control. Preliminary microarray data demonstrated NS5A-related increases in mRNA levels for TGFB1-induced anti-apoptotic factor 1 and chemokine ligand 25 mRNA. Both of these genes enhance resistance to apoptosis, and CC ligand 25 does so in CD4+ T cells.

FIG. 8—Dose-Dependent HIV Inhibition by the NS5A Protein. Left panel—NS5A-expressing Jurkat cells; right panel—vector control Jurkat cells. HIV replication is measured by p24 antigen levels on days 2-6 (D2-D6). Amounts of doxycycline, which inversely relate to NS5A production, are shown in μg/ml.

FIG. 9—Both IFN-R and IFN-S GBV-C NS5A Inhibit HIV Replication. HIV replication is measured by p24 antigen levels on days 2-6 (D2-D6). VC=vector control; GFP—vector expression GFP only; IFN-S=interferon sensitive NS5A; IFN-R=interferon resistant NS5A.

FIG. 10—Anti-SDF-1 Blocks NSF5A-Mediated Inhibition of HIV Replication. Results reported as percent increase in HIV replication when cultures are incubated with anti-SDF-1 neutralizing antibody as compared to isotype control antibody. IFN-R=interferon resistant NS5A; IFN-R-GFP=interferon resistant NS5A linked to GFP; IFN-S-GFP=interferon sensitive NS5A linked to GFP.

FIGS. 11A-C—NS5A Inhibits Multiple Distinct HIV Strains. HIV replication is measured by p24 antigen levels on days 2-6 (D2-D6). VC-GFP=vector control expression GFP; IFN-R=interferon resistant NS5A; IFN-R-GFP=interferon resistant NS5A linked to GFP; IFN-S-GFP=interferon sensitive NS5A linked to GFP.

FIG. 12—Fragments of NS5A That Have Been Stably Expressed in Jurkat Cells. Shaded bars indicate fusions or fragments.

FIG. 13—Fragments of NS5A That Inhibit HIV Replication. Shaded bars inhibit HIV; open bars do not inhibit HIV.

FIG. 14—Doxycycline-Repressed Expression of NS5A. Lanes are labeled with amounts of doxycycline (μg/ml); arrows indicate NS5A or mutants (mu NS5A).

FIG. 15—Percent Inhibition of HIV Replication by NS5A Fragments. Various fragments identified by residues of NS5A remaining, and their ability to inhibit HIV replication (by p24 antigen levels) on day 6 after infection.

FIG. 16—Fragments of NS5A That Inhibit HIV Replication. Shaded bars inhibit HIV; open bars do not inhibit HIV; lined bars not yet tested.

FIG. 17—R 152-237 NS5A inhibits HIV when expressed in Jurkat cells. By deduction, it appears that 152-182 is the minimal sequence required for HIV inhibition. Note that the latter sequence is conserved (IFN-R and IFN-S) GBV-C NS5A, and that there are multiple potential phosphorylation sites.

DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

Anti-retroviral medications suppress viral replication in HIV disease, yet they have failed to eradicate the virus from the body due to the multi-faceted nature of HIV infection, as well as the complexities of the immune system. Methods are being developed that both prevent infection and boost the immune system to keep it functioning at a level where it can assist in fighting HIV infection.

The present inventors have previously reported on methods and compositions for therapeutic and/or prophylatic treatment of HIV infection, including GBV-C envelope proteins, in particular GBV-C envelope protein E2 (E2). More specifically, the inventors have shown that HIV-infected subjects that are co-infected with GB virus C (GBV-C) typically have reduced mortality and slower progression to AIDS as compared to HIV-infected subjects without GBV-C co-infection (PCT/US2004/017706). Infection of peripheral blood mononuclear cells (PBMCs) with GBV-C and HIV results in inhibition of HIV-1 replication. GBV-C infection typically inhibits HIV by inducing β-chemokines and reducing expression of the HIV co-receptor CCR5, explaining part of the beneficial clinical findings of GBV-C on HIV disease progression. The inventors also described a therapeutic use for antibodies and/or binding agents that bind GBV-C proteins (e.g., envelope proteins), in particular, the E2 protein, and similar antigens used for producing these antibodies or binding agents (PCT/US03/33925).

The inventors now demonstrate a unique role for the NS5A protein of GBV-C, as well as NS5A's from other flaviviruses, in the inhibition of HIV replication. Various aspects of the invention are described below.

Flaviviruses

A. Family

With a total of 69 pathogens in its ranks, Flaviviridae contains a myriad of viruses that cause disease in humans. Foremost among these is Yellow Fever Virus, the type virus of the Flaviviridae, from which the family begets its name (/1avus in Latin means “yellow”). Flaviviruses have been subdivided by the ICTV into three genera: Flavivirus, Pestivirus and Hepacivirus.

The Flavivirus genus contains several dangerous viruses including yellow fever virus, dengue fever virus, and Japanese encaphilitis (JE) virus. The Pestivirus genus is home to the three serotypes of bovine viral diarrhea, but no known human pathogens. The genus Hepacivirus consists of hepatitis C virus and its relatives.

Flavivirus genomes consist of a monopartite (i.e., one piece of) linear, single-stranded, positive sense RNA. Because the RNA is positive sense, the nucleic acid itself is capable of instigating an infection in the appropriate host cells. The total genome can range from 10 to 11 kilobase pairs. The genome 3′ terminus is not polyadenylated. The 5′ end has a methylated nucleotide cap (allows for translation) or a genome-linked protein (VPg). Pestivirus genomes are reported to be 12.5 kb in length. Like the Flavivirus genus, no poly-A tail exists on the 3′ end of the RNA, however, Pestivirus genus members lack a 5′ cap. In both genera, structural genes are found towards the 5′ end of the RNA. Both the Pestivirus and Hepacivirus genera contain internal ribosomal entry sites (IRES) that provide a site of translation initiation for host ribosomes. This is in contrast to the Flavivirus genus that uses the technique of ribosomal scanning to commence protein synthesis.

Under the EM, virions appear roughly as spheres (some experts say they're “pleomorphic”), 40-65 nm in diameter. What can be seen under the microscope is the virus's lipid envelope, which it obtains from host cells during egress (leaving the cell). Underneath the envelope can be found an icosahedral capsid coat approximately 25-30 nm in diameter.

All members of the Flavivirus genus are transmitted by arthropods (i.e., mosquitoes and ticks) while Hepatitis C is spread parenterally (i.e., through contaminated bodily fluids). A key feature for viral transmission in Flaviviruses is that they are capable of reproducing in their vector. Without the ability to replicate in the vector, they would not remain viable to be passed from one host to the next.

B. GBV-C

Like other members of the Flaviviridae, GBV-C is a positive-strand RNA virus that encodes a single long open reading frame (Leary et al., 1996). GBV-C does not cause acute or chronic hepatitis, yet it is the family member most closely related to HCV, the cause of hepatitis C. Sequences of GBV-C have been previously reported, for example in U.S. Pat. No. 5,874,563, which is specifically incorporated by reference. In particular, an infectious GBV-C clone has been described in the PCT application WO 01/77157, which is incorporated herein by reference.

The GBV-C polyprotein is predicted to be cleaved into two envelope proteins (E1 and E2, referred to collectively as GBV-C envelope protein), an RNA helicase, a trypsin-like serine protease, and an RNA-dependent RNA polymerase. A major difference between GBV-C and HCV is in the amino terminus of the polyprotein. In many isolates, this region is truncated, and no core (or nucleocapsid) protein is present (Simons et al., 1995; Xiang et al., 1999). In vitro translation experiments suggest that the AUG immediately upstream of the putative El protein is preferentially used to initiate translation, although there may be as many as four AUG's in frame with the polyprotein upstream of this AUG (Simons et al., 1996).

The site of GBV-C replication has not been clearly identified, but it appears that replication in the hepatocyte, if it occurs, is not the primary source of virus in infected individuals (Laskus et al., 1998; Pessoa et al., 1998; Seipp et al., 1999). Recently, there were reports that human peripheral blood mononuclear cells (PBMC's) and interferon-resistant Daudi cells are permissive for GBV-C replication (Fogeda et al., 1999; Shimizu, 1999). In addition, transient replication of GBV-C was described in MT-2 cells (a human T-cell line), and PH5CH (a human hepatocyte line immortalized with simian virus 40 large T antigen) (Seipp et al., 1999).

C. Other Flavivirus NS5A's

Other Flaviviruses contain NS5A's that can be used in accordance with the present invention. These viruses include DEN1-4, YFV, TBEV, WNV, CSFV, BVDV, GBV-A, GBV-B, HGV, HCV2a, HCV3a, HCV2b, HCV1a, HCV1c and HCV1b.

GBV-C Polypeptides

In certain aspects, the invention is directed to the the NS5A polypeptide of GBV-C virus, or a peptide or polypeptide derived there from SEQ ID NO:2 shows the NS5A translated product of SEQ ID NO:1 (cDNA). It is contemplated that the compositions and methods disclosed herein may be utilized to express all or part of SEQ ID NO:2 and derivatives thereof. In certain embodiments, compositions of the invention may include the nucleic acids encoding the peptides as set forth in SEQ ID NO:1 or 3. Determination of which protein or DNA molecules inhibit HIV may be achieved using functional assays measuring HIV replication and infectivity, which are familiar to those of skill in the art. The structure of the various polypeptides or peptides can be modeled or resolved by computer modeling, NMR, or x-ray crystallography. Such structures may be used to engineer derivatives of the various NS5A protein.

Exemplary accession nos. (incorporated by reference) for other NS5A's are as follows: Virus Accession No. Virus Accession No. West Nile DQ318019 Dengue 1-4 AY66269 Yellow fever NC002031 HCV 1a AF011753 AY603338 1b AF333324 BVDV AF502399 1c D14853 Dengue 1-4 M878512 2a D00944 M14931 2b D10988 M20558 3a AF046866

A. Variants of GBV-C NS5A Polypeptides

Embodiments of the invention include various GBV-C NS5A polypeptides, peptides, and derivatives thereof. Amino acid sequence variants of a polypeptide can be substitutional, insertional or deletion variants. Deletion variants lack one or more residues of the native protein that are not essential for function or immunogenic activity. Insertional mutants typically involve the addition of material at a non-terminal point in the polypeptide. This may include the insertion of an immunoreactive epitope or simply a single residue. Terminal additions, called fusion proteins, are discussed below.

Substitutional variants typically contain the exchange of one amino acid for another at one or more sites within the protein, and may be designed to modulate one or more properties of the polypeptide, such as stability against proteolytic cleavage, without the loss of other functions or properties. Substitutions of this kind preferably are conservative, that is, one amino acid is replaced with one of similar shape and charge. Conservative substitutions are well known in the art and include, for example, the changes of: alanine to serine; arginine to lysine; asparagine to glutamine or histidine; aspartate to glutamate; cysteine to serine; glutamine to asparagine; glutamate to aspartate; glycine to proline; histidine to asparagine or glutamine; isoleucine to leucine or valine; leucine to valine or isoleucine; lysine to arginine; methionine to leucine or isoleucine; phenylalanine to tyrosine, leucine or methionine; serine to threonine; threonine to serine; tryptophan to tyrosine; tyrosine to tryptophan or phenylalanine; and valine to isoleucine or leucine.

The term “biologically functional equivalent” is well understood in the art and is further defined in detail herein. Accordingly, sequences that have between about 70% and about 80%; or more preferably, between about 81% and about 90%; or even more preferably, between about 91% and about 99%; of amino acids that are identical or functionally equivalent to the amino acids of GBV-C NS5A polypeptides, for example SEQ ID NO:2, provided the biological activity of the protein or peptide is maintained.

The term “functionally equivalent codon” is used herein to refer to codons that encode the same amino acid, such as the six codons for arginine or serine, and also refers to codons that encode biologically equivalent amino acids (see Table 1, below).

Certain embodiments of the invention include various peptides or polypeptides of the NS5A protein. For example, all or part of a GBV-C NS5A protein as set forth in SEQ ID NO:2 may be used in various embodiments of the invention. In certain embodiments, a fragment of the NS5A protein may comprise, but is not limited to about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25, about 26, about 27, about 28, about 29, about 30, about 31, about 32, about 33, about 34, about 35, about 36, about 37, about 38, about 39, about 40, about 41, about 42, about 43, about 44, about 45, about 46, about 47, about 48, about 49, about 50, about 51, about 52, about 53, about 54, about 55, about 56, about 57, about 58, about 59, about 60, about 61, about 62, about 63, about 64, about 65, about 66, about 67, about 68, about 69, about 70, about 71, about 72, about 73, about 74, about 75, about 76, about 77, about 78, about 79, about 80, about 81, about 82, about 83, about 84, about 85, about 86, about 87, about 88, about 89, about 90, about 91, about 92, about 93, about 94, about 95, about 96, about 97, about 98, about 99, about 100, about 110, about 120, about 130, about 140, about 150, about 160, about 170, about 180, about 190, about 200, about 210, about 220, about 230, about 240, about 250, about 275, about 300, about 325, about 350, about 375, about 400, about 415, and any range derivable therein.

It also will be understood that amino acid and nucleic acid sequences may include additional residues, such as additional N— or C-terminal amino acids or 5′ or 3′ sequences, and yet still be essentially as set forth in one of the sequences disclosed herein, so long as the sequence meets the criteria set forth above, including the maintenance of biological activity (e.g., immunogenicity) where protein expression is concerned. The addition of terminal sequences particularly applies to nucleic acid sequences that may, for example, include various non-coding sequences flanking either of the 5′ or 3′ portions of the coding region.

The following is a discussion based upon changing of the amino acids of an NS5A polypeptide or peptide to create an equivalent, or even an improved, second-generation molecule. For example, certain amino acids may be substituted for other amino acids in a protein structure without appreciable loss of interactive binding capacity with structures such as, for example, antigen-binding regions of antibodies or binding sites on substrate molecules. Since it is the interactive capacity and nature of a protein that defines that protein's biological functional activity, certain amino acid substitutions can be made in a protein sequence, and in its underlying DNA or RNA coding sequence, and nevertheless produce a protein with like properties. It is thus contemplated by the inventors that various changes may be made in the DNA or RNA sequences of genes or coding regions without appreciable loss of their biological utility or activity, as discussed herein. Table 1 shows the codons that encode particular amino acids. TABLE 1 CODON TABLE Amino Acids Codons Alanine Ala A GCA GCC GCG GCU Cysteine Cys C UGC UGU Aspartic acid Asp D GAC GAU Glutamic acid Glu E GAA GAG Phenylalanine Phe F UUC UUU Glycine Gly G GGA GGC GGG GGU Histidine His H CAC CAU Isoleucine Ile I AUA AUC AUU Lysine Lys K AAA AAG Leucine Leu L UUA UUG CUA CUC CUG CUU Methionine Met M AUG Asparagine Asn N AAC AAU Proline Pro P CCA CCC CCG CCU Glutamine Gln Q CAA CAG Arginine Arg R AGA AGG CGA CGC CGG CGU Serine Ser S AGC AGU UCA UCC UCG UCU Threonine Thr T ACA ACC ACG ACU Valine Val V GUA GUC GUG GUU Tryptophan Trp W UGG Tyrosine Tyr Y UAC UAU

In making such changes, the hydropathic index of amino acids may be considered. The importance of the hydropathic amino acid index in conferring interactive biologic function on a protein is generally understood in the art (Kyte and Doolittle, 1982). It is accepted that the relative hydropathic character of the amino acid contributes to the secondary structure of the resultant protein, which in turn defines the interaction of the protein with other molecules, for example, enzymes, substrates, receptors, DNA, antibodies, antigens, and the like.

It also is understood in the art that the substitution of like amino acids can be made effectively on the basis of hydrophilicity. U.S. Patent 4,554,101, incorporated herein by reference, states that the greatest local average hydrophilicity of a protein, as governed by the hydrophilicity of its adjacent amino acids, correlates with a biological property of the protein.

It is understood that an amino acid substituted for another having a similar hydrophilicity value still produces a biologically equivalent and immunologically equivalent protein.

In certain embodiments, an NS5A polypeptide may be a fusion protein. Fusion proteins may alter the characteristics of a given polypeptide, such antigenicity or purification characteristics. A fusion protein is a specialized type of insertional variant. This molecule generally has all or a substantial portion of the native molecule, linked at the N— or C-terminus, to all or a portion of a second polypeptide. For example, fusions typically employ leader sequences from other species to permit the recombinant expression of a protein in a heterologous host. Another useful fusion includes the addition of an immunologically active domain, such as an antibody epitope, to facilitate purification of the fusion protein. Inclusion of a cleavage site at or near the fusion junction will facilitate removal of the extraneous polypeptide after purification. Other useful fusions include linking of functional domains, such as active sites from enzymes such as a hydrolase, glycosylation domains, cellular targeting signals, or transmembrane regions.

B. In vitro Production of NS5A Polypeptides or Peptides

Various types of expression vectors are known in the art that can be used for the production of protein products. Following transfection with a expression vector, a cell in culture, e.g., a primary mammalian cell, a recombinant product may be prepared in various ways. A host cell strain may be chosen that modulates the expression of the inserted sequences, or that modifies and processes the gene product in the manner desired. Such modifications (e.g., glycosylation) and processing (e.g., cleavage) of protein products may be important for the function of the protein. Different host cells have characteristic and specific mechanisms for the post-translational processing and modification of proteins. Appropriate cell lines or host systems can be chosen to insure the correct modification and processing of the foreign protein expressed. In order for the cells to be kept viable while in vitro and in contact with the expression construct, it is necessary to ensure that the cells maintain contact with the correct ratio of oxygen and carbon dioxide and nutrients but are protected from microbial contamination. Cell culture techniques are well documented (for exemplary methods see Freshney, 1992).

Animal cells can be propagated in vitro in two modes: as non-anchorage-dependent cells growing in suspension throughout the bulk of the culture or as anchorage-dependent cells requiring attachment to a solid substrate for their propagation (i.e., a monolayer type of cell growth).

Non-anchorage dependent or suspension cultures from continuous established cell lines are the most widely used means of large-scale production of cells and cell products. However, suspension cultured cells have limitations, such as tumorigenic potential and lower protein production than adherent cells.

In further aspects of the invention, other protein production methods known in the art may be used, including but not limited to prokaryotic, yeast, and other eukaryotic hosts such as insect cells and the like.

Because of their relatively small size, the peptides of the invention can also be synthesized in solution or on a solid support in accordance with conventional techniques. Various automatic synthesizers are commercially available and can be used in accordance with known protocols. See, for example, Stewart and Young, (1984); Tam et al., (1983); Merrifield, (1986); and Barany and Merrifield (1979), each incorporated herein by reference. Short peptide sequences, or libraries of overlapping peptides, usually from about 6 up to about 35 to 50 amino acids, which correspond to the selected regions described herein, can be readily synthesized and then screened in screening assays designed to identify reactive peptides.

C. Protein Purification

It may be desirable to purify NS5A polypeptides and peptides, or variants and derivatives thereof. Protein purification techniques are well known to those of skill in the art. These techniques involve, at one level, the crude fractionation of the cellular milieu to polypeptide and non-polypeptide fractions. Having separated the polypeptide from other proteins, the polypeptide of interest may be further purified using chromatographic and electrophoretic techniques to achieve partial or complete purification (or purification to homogeneity). Analytical methods particularly suited to the preparation of a pure peptide are ion-exchange chromatography, hydrophobic interaction chromatography, exclusion chromatography; polyacrylamide gel electrophoresis; isoelectric focusing. A particularly efficient method of purifying peptides is fast protein liquid chromatography (FPLC).

Certain aspects of the present invention concern the purification, and in particular embodiments, the substantial purification, of an encoded protein or peptide. The term “purified protein or peptide” as used herein, is intended to refer to a composition, isolatable from other components, wherein the protein or peptide is purified to any degree relative to its naturally obtainable state. A purified protein or peptide therefore also refers to a protein or peptide, free from the environment in which it may naturally occur.

Generally, “purified” will refer to a protein or peptide composition that has been subjected to fractionation to remove various other components, and which composition substantially retains its expressed biological activity. Where the term “substantially purified” is used, this designation will refer to a composition in which the protein or peptide forms the major component of the composition, such as constituting about 50%, about 60%, about 70%, about 80%, about 90%, about 95% or more of the proteins in the composition.

Various methods for quantifying the degree of purification of the protein or peptide will be known to those of skill in the art in light of the present disclosure. These include, for example, determining the specific activity of an active fraction, or assessing the amount of polypeptides within a fraction by SDS/PAGE analysis. A preferred method for assessing the purity of a fraction is to calculate the specific activity of the fraction, to compare it to the specific activity of the initial extract, and to thus calculate the degree of purity, herein assessed by a “-fold purification number.” The actual units used to represent the amount of activity will, of course, be dependent upon the particular assay technique chosen to follow the purification and whether or not the expressed protein or peptide exhibits a detectable activity.

There is no general requirement that the protein or peptide always be provided in their most purified state. Indeed, it is contemplated that less substantially purified products will have utility in certain embodiments. Partial purification may be accomplished by using fewer purification steps in combination, or by utilizing different forms of the same general purification scheme.

Flavivirus Polynucleotides

Certain embodiments of the invention include Flavivirus NS5A polynucleotides or nucleic acid molecules and fragments thereof. The polynucleotides of the invention may be isolated and purified from Flavivirus or cells infected or transfected with Flavivirus polynucleotides. The term isolated indicating they are free or substantially free from total viral or cellular genomic RNA or DNA, and proteins. It is contemplated that an isolated and purified Flavivirus nucleic acid molecule may take the form of RNA or DNA. A Flavivirus nucleic acid molecule refers to an RNA or DNA molecule that is capable of yielding all or part of a Flavivirus NS5A from a transfected cell.

When the present application refers to the function or activity of an infectious Flavivirus that is encoded by a Flavivirus polynucleotide, it is meant that the polynucleotide encodes a molecule that has the ability to propagate an infectious Flavivirus virus particle from a cell. It is contemplated that a Flavivirus polynucleotide may refer to a Flavivirus RNA transcript that is able to propagate an infectious Flavivirus virus particle after introduction to a cell or to a Flavivirus expression construct, clone, or vector composed of double-stranded DNA or DNA/RNA hybrid that is similarly capable,or a doublestranded DNA that is similiarly capable following in vitro transcription.

The term “cDNA” is intended to refer to DNA prepared using RNA as a template. The advantage of using a cDNA, as opposed to genomic RNA or an RNA transcript is stability and the ability to manipulate the sequence using recombinant DNA technology (See Maniatis, 1990; Ausubel, 1996). There may be times when the full or partial genomic sequence is preferred.

It also is contemplated that a given Flavivirus may be represented by natural variants or strains that have slightly different nucleic acid sequences but, nonetheless, encode the same viral polypeptides (see Table 1 above). Consequently, the present invention also encompasses derivatives of Flavivirus with minimal amino acid changes in its viral proteins, but that possesses the same activities.

The term “gene” is used for simplicity to refer to the nucleic acid giving rise to a functional protein, polypeptide, or peptide-encoding unit. As will be understood by those in the art, this functional term includes genomic sequences, cDNA sequences, and smaller engineered gene segments that express, or may be adapted to express, proteins, polypeptides, domains, peptides, fusion proteins, and mutants. The nucleic acid molecule encoding Flavivirus may contain a contiguous nucleic acid sequence encoding one or more Flavivirus genes and regulatory regions and be of the following lengths: about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 441, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, 1000, 1010, 1020, 1030, 1040, 1050, 1060, 1070, 1080, 1090, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800, 2900, 3000, 3100, 3200, 3300, 3400, 3500, 3600, 3700, 3800, 3900, 4000, 4100, 4200, 4300, 4400, 4500, 4600, 4700, 4800, 4900, 5000, 5100, 5200, 5300, 5400, 5500, 5600, 5700, 5800, 5900, 6000, 6100, 6200, 6300, 6400, 6500, 6600, 6700, 6800, 6900, 7000, 7100, 7200, 7300, 7400, 7500, 7600, 7700, 7800, 7900, 8000, 8100, 8200, 8300, 8400, 8500, 8600, 8700, 8800, 8900, 9000, 9100, 9200, 9300, 9400, 10,000 or more nucleotides, nucleosides, or base pairs. Such sequences may be identical or complementary to all or part of SEQ ID NO:1.

In particular embodiments, the invention concerns isolated nucleic acid segments and recombinant vectors incorporating DNA sequences that encode Flavivirus NS5A polypeptides or peptides. Such vectors used in the present invention, regardless of the length of the coding sequence itself, may be combined with other DNA or RNA sequences, such as promoters, polyadenylation signals, additional restriction enzyme sites, multiple cloning sites, other coding segments, and the like, such that their overall length may vary considerably. It is therefore contemplated that a nucleic acid fragment of almost any length may be employed, with the total length preferably being limited by the ease of preparation and use in the intended recombinant DNA protocol.

In a non-limiting example, one or more nucleic acid constructs may be prepared that include a contiguous stretch of nucleotides identical to or complementary to a Flavivirus genome. A nucleic acid construct may be about 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1,000, 2,000, 3,000, 4,000, 5,000, 6,000, 7,000, 8,000, 9,000, and 9,400, nucleotides in length, as well as constructs of greater size, up to and including chromosomal sizes (including all intermediate lengths and intermediate ranges), given the advent of nucleic acids constructs such as a yeast artificial chromosome are known to those of ordinary skill in the art. It will be readily understood that “intermediate lengths” and “intermediate ranges,” as used herein, means any length or range including or between the quoted values (i.e., all integers including and between such values). Non-limiting examples of intermediate lengths include about 11, about 12, about 13, about 16, about 17, about 18, about 19, etc.; about 21, about 22, about 23, etc.; about 31, about 32, etc.; about 51, about 52, about 53, etc.; about 101, about 102, about 103, etc.; about 151, about 152, about 153, etc.

The nucleic acid segments used in the present invention encompass biologically functional and/or immunogenically equivalent Flavivirus NS5A proteins and peptides. Such sequences may arise as a consequence of codon redundancy and functional equivalency that are known to occur naturally within nucleic acid sequences and the proteins thus encoded. Alternatively, functionally and immunologically equivalent proteins or peptides may be created via the application of recombinant DNA technology, in which changes in the protein structure may be engineered, based on considerations of the properties of the amino acids being exchanged. Changes designed by human may be introduced through the application of site-directed mutagenesis techniques, e.g., to introduce improvements to the antigenicity of the protein.

A. Vectors Encoding Flavivirus

The present invention encompasses the use of vectors to encode for all or part of one or more Flavivirus NS5A polypeptides, including an infectious Flavivirus. The term “vector” is used to refer to a carrier nucleic acid molecule into which a nucleic acid sequence can be inserted for introduction into a cell where it can be replicated. A nucleic acid sequence can be “exogenous,” which means that it is foreign to the cell into which the vector is being introduced or that the sequence is homologous to a sequence in the cell but in a position within the host cell nucleic acid in which the sequence is ordinarily not found. Vectors include plasmids, cosmids, viruses (bacteriophage, animal viruses, and plant viruses), and artificial chromosomes (e.g., YACs). In particular embodiments, gene therapy or immunization vectors are contemplated. One of skill in the art would be well equipped to construct a vector through standard recombinant techniques, which are described in Maniatis et al., 1990 and Ausubel et al., 1996, both incorporated herein by reference.

The term “expression vector” or “expression construct” refers to a vector containing a nucleic acid sequence coding for at least part of a gene product capable of being transcribed. In some cases, RNA molecules are then translated into a protein, polypeptide, or peptide. In other cases, these sequences are not translated, for example, in the production of antisense molecules or ribozymes. Expression vectors can contain a variety of “control sequences,” which refer to nucleic acid sequences necessary for the transcription and possibly translation of an operably linked coding sequence in a particular host organism. In addition to control sequences that govern transcription and translation, vectors and expression vectors may contain nucleic acid sequences that serve other functions as well and are described infra. It is contemplated that an infectious Flavivirus particle of the present invention may arise from a vector containing Flavivirus sequence or RNA encoding Flavivirus sequence into a cell. Either of these, or any other nucleic acid molecules of the present invention may be constructed with any of the following nucleic acid control sequences. Thus, the full-length RNA transcript may contain the benefit of recombinant DNA technology such that it contains exogenous control sequences or genes.

1. Promoters and Enhancers

A “promoter” is a control sequence that is a region of a nucleic acid sequence at which initiation and rate of transcription are controlled. It may contain genetic elements at which regulatory proteins and molecules may bind such as RNA polymerase and other transcription factors. The phrases “operatively positioned,” “operatively linked,” “under control,” and “under transcriptional control” means that a promoter is in a correct functional location and/or orientation in relation to a nucleic acid sequence to control transcriptional initiation and/or expression of that sequence. A promoter may or may not be used in conjunction with an “enhancer,” which refers to a cis-acting regulatory sequence involved in the transcriptional activation of a nucleic acid sequence.

A promoter may be one naturally associated with a gene or sequence, as may be obtained by isolating the 5′ non-coding sequences located upstream of the coding segment and/or exon. Such a promoter can be referred to as “endogenous.” Similarly, an enhancer may be one naturally associated with a nucleic acid sequence, located either downstream or upstream of that sequence. Alternatively, certain advantages will be gained by positioning the coding nucleic acid segment under the control of a recombinant or heterologous promoter, which refers to a promoter that is not normally associated with a nucleic acid sequence in its natural environment. A recombinant or heterologous enhancer refers also to an enhancer not normally associated with a nucleic acid sequence in its natural environment. Such promoters or enhancers may include promoters or enhancers of other genes, and promoters or enhancers isolated from any other prokaryotic, viral, or eukaryotic cell, and promoters or enhancers not “naturally occurring,” i.e., containing different elements of different transcriptional regulatory regions, and/or mutations that alter expression. In addition to producing nucleic acid sequences of promoters and enhancers synthetically, sequences may be produced using recombinant cloning and/or nucleic acid amplification technology, including PCR™, in connection with the compositions disclosed herein (see U.S. Pat. No. 4,683,202 and U.S. Pat. No. 5,928,906, each incorporated herein by reference). Furthermore, it is contemplated the control sequences that direct transcription and/or expression of sequences within non-nuclear organelles such as mitochondria, chloroplasts, and the like, can be employed as well.

Naturally, it will be important to employ a promoter and/or enhancer that effectively directs the expression of the nucleic acid segment in the cell type, organelle, and organism chosen for expression. Those of skill in the art of molecular biology generally know the use of promoters, enhancers, and cell type combinations for protein expression, for example, see Sambrook et al. (2001), incorporated herein by reference. The promoters employed may be constitutive, tissue-specific, inducible, and/or useful under the appropriate conditions to direct high level expression of the introduced DNA segment, such as is advantageous in the large-scale production of recombinant proteins and/or peptides. The promoter may be heterologous or exogenous, i.e., from a different source the Flavivirus sequence. In some examples, a prokaryotic promoter is employed for use with in vitro transcription of a desired sequence. Prokaryotic promoters for use with many commercially available systems include T7, T3, and Sp6.

Table 2 lists several elements/promoters that may be employed, in the context of the present invention, to regulate the expression of a gene. This list is not intended to be exhaustive of all the possible elements involved in the promotion of expression but, merely, to be exemplary thereof. Table 3 provides examples of inducible elements, which are regions of a nucleic acid sequence that can be activated in response to a specific stimulus. TABLE 2 Promoter and/or Enhancer Promoter/Enhancer References Immunoglobulin Heavy Chain Banerji et al., 1983; Gilles et al., 1983; Grosschedl et al., 1985; Atchinson et al., 1986, 1987; Imler et al., 1987; Weinberger et al., 1984; Kiledjian et al., 1988; Porton et al.; 1990 Immunoglobulin Light Chain Queen et al., 1983; Picard et al., 1984 T-Cell Receptor Luria et al., 1987; Winoto et al., 1989; Redondo et al.; 1990 HLA DQ a and/or DQ β Sullivan et al., 1987 β-Interferon Goodbourn et al., 1986; Fujita et al., 1987; Goodbourn et al., 1988 Interleukin-2 Greene et al., 1989 Interleukin-2 Receptor Greene et al., 1989; Lin et al., 1990 MHC Class II 5 Koch et al., 1989 MHC Class II HLA-DRa Sherman et al., 1989 β-Actin Kawamoto et al., 1988; Ng et al.; 1989 Muscle Creatine Kinase (MCK) Jaynes et al., 1988; Horlick et al., 1989; Johnson et al., 1989 Prealbumin (Transthyretin) Costa et al., 1988 Elastase I Omitz et al., 1987 Metallothionein (MTII) Karin et al., 1987; Culotta et al., 1989 Collagenase Pinkert et al., 1987; Angel et al., 1987 Albumin Pinkert et al., 1987; Tronche et al., 1989, 1990 α-Fetoprotein Godbout et al., 1988; Campere et al., 1989 γ-Globin Bodine et al., 1987; Perez-Stable et al., 1990 β-Globin Trudel et al., 1987 c-fos Cohen et al., 1987 c-HA-ras Triesman, 1986; Deschamps et al., 1985 Insulin Edlund et al., 1985 Neural Cell Adhesion Molecule Hirsh et al., 1990 (NCAM) α₁-Antitrypain Latimer et al., 1990 H2B (TH2B) Histone Hwang et al., 1990 Mouse and/or Type I Collagen Ripe et al., 1989 Glucose-Regulated Proteins Chang et al., 1989 (GRP94 and GRP78) Rat Growth Hormone Larsen et al., 1986 Human Serum Amyloid A (SAA) Edbrooke et al., 1989 Troponin I (TN I) Yutzey et al., 1989 Platelet-Derived Growth Factor Pech et al., 1989 (PDGF) Duchenne Muscular Dystrophy Klamut et al., 1990 SV40 Banerji et al., 1981; Moreau et al., 1981; Sleigh et al., 1985; Firak et al., 1986; Herr et al., 1986; Imbra et al., 1986; Kadesch et al., 1986; Wang et al., 1986; Ondek et al., 1987; Kuhl et al., 1987; Schaffner et al., 1988 Polyoma Swartzendruber et al., 1975; Vasseur et al., 1980; Katinka et al., 1980, 1981; Tyndell et al., 1981; Dandolo et al., 1983; de Villiers et al., 1984; Hen et al., 1986; Satake et al., 1988; Campbell and/or Villarreal, 1988 Retroviruses Kriegler et al., 1982, 1983; Levinson et al., 1982; Kriegler et al., 1983, 1984a, b, 1988; Bosze et al., 1986; Miksicek et al., 1986; Celander et al., 1987; Thiesen et al., 1988; Celander et al., 1988; Chol et al., 1988; Reisman et al., 1989 Papilloma Virus Campo et al., 1983; Lusky et al., 1983; Spandidos and/or Wilkie, 1983; Spalholz et al., 1985; Lusky et al., 1986; Cripe et al., 1987; Gloss et al., 1987; Hirochika et al., 1987; Stephens et al., 1987; Glue et al., 1988 Hepatitis B Virus Bulla et al., 1986; Jameel et al., 1986; Shaul et al., 1987; Spandau et al., 1988; Vannice et al., 1988 Human Immunodeficiency Virus Muesing et al., 1987; Hauber et al., 1988; Jakobovits et al, 1988; Feng et al., 1988; Takebe et al., 1988; Rosen et al., 1988; Berkhout et al., 1989; Laspia et al., 1989; Sharp et al., 1989; Braddock et al., 1989 Cytomegalovirus (CMV) Weber et al., 1984; Boshart et al., 1985; Foecking et al., 1986 Gibbon Ape Leukemia Virus Holbrook et al., 1987; Quinn et al., 1989

TABLE 3 Inducible Elements Element Inducer References MT II Phorbol Ester (TFA) Palmiter et al., 1982; Heavy metals Haslinger et al., 1985; Searle et al., 1985; Stuart et al., 1985; Imagawa et al., 1987, Karin et al., 1987; Angel et al., 1987b; McNeall et al., 1989 MMTV (mouse mammary tumor Glucocorticoids Huang et al., 1981; Lee et virus) al., 1981; Majors et al., 1983; Chandler et al., 1983; Lee et al., 1984; Ponta et al., 1985; Sakai et al., 1988 β-Interferon poly(rI) × poly(rc) Tavernier et al., 1983 Adenovirus 5 E2 E1A Imperiale et al., 1984 Collagenase Phorbol Ester (TPA) Angel et al., 1987a Stromelysin Phorbol Ester (TPA) Angel et al., 1987b SV40 Phorbol Ester (TPA) Angel et al., 1987b Murine MX Gene Interferon, Newcastle Hug et al., 1988 Disease Virus GRP78 Gene A23187 Resendez et al., 1988 α-2-Macroglobulin IL-6 Kunz et al., 1989 Vimentin Serum Rittling et al., 1989 MHC Class I Gene H-2κb Interferon Blanar et al., 1989 HSP70 E1A, SV40 Large T Taylor et al., 1989, 1990a, Antigen 1990b Proliferin Phorbol Ester-TPA Mordacq et al., 1989 Tumor Necrosis Factor PMA Hensel et al., 1989 Thyroid Stimulating Thyroid Hormone Chatterjee et al., 1989 Hormone α Gene

The identity of tissue-specific promoters or elements, as well as assays to characterize their activity, is well known to those of skill in the art. Examples of such regions include the human LIMK2 gene (Nomoto et al. 1999), the somatostatin receptor 2 gene (Kraus et al., 1998), murine epididymal retinoic acid-binding gene (Lareyre et al., 1999), human CD4 (Zhao-Emonet et al., 1998), mouse alpha2 (XI) collagen (Tsumaki, et al., 1998), DIA dopamine receptor gene (Lee, et al., 1997), insulin-like growth factor II (Wu et al., 1997), human platelet endothelial cell adhesion molecule-I (Almendro et al., 1996).

2. Initiation Signals and Internal Ribosome Binding Sites

A specific initiation signal also may be required for efficient translation of coding sequences. These signals include the ATG initiation codon or adjacent sequences. Exogenous translational control signals, including the ATG initiation codon, may need to be provided. One of ordinary skill in the art would readily be capable of determining this 15 and providing the necessary signals. It is well known that the initiation codon must be “in-frame” with the reading frame of the desired coding sequence to ensure translation of the entire insert. The exogenous translational control signals and initiation codons can be either natural or synthetic. The efficiency of expression may be enhanced by the inclusion of appropriate transcription enhancer elements.

In certain embodiments of the invention, the use of internal ribosome entry sites (IRES) elements are used to create multigene, or polycistronic, messages. IRES elements are able to bypass the ribosome-scanning model of 5′ methylated Cap dependent translation and begin translation at internal sites (Pelletier and Sonenberg, 1988). IRES elements from two members of the picornavirus family (polio and encephalomyocarditis) have been described (Pelletier and Sonenberg, 1988), as well an IRES from a mammalian message (Macejak and Sarnow, 1991). IRES elements can be linked to heterologous open reading frames. Multiple open reading frames can be transcribed together, each separated by an IRES, creating polycistronic messages. By virtue of the IRES element, each open reading frame is accessible to ribosomes for efficient translation. Multiple genes can be efficiently expressed using a single promoter/enhancer to transcribe a single message (see U.S. Pat. No. 5,925,565 and 5,935,819, herein incorporated by reference).

3. Multiple Cloning Sites

Vectors can include a multiple cloning site (MCS), which is a nucleic acid region that contains multiple restriction enzyme sites, any of which can be used in conjunction with standard recombinant technology to digest the vector. (See Carbonelli et al., 1999, Levenson et al., 1998, and Cocea, 1997, incorporated herein by reference.) “Restriction enzyme digestion” refers to catalytic cleavage of a nucleic acid molecule with an enzyme that functions only at specific locations in a nucleic acid molecule. Many of these restriction enzymes are commercially available. Use of such enzymes is widely understood by those of skill in the art. Frequently, a vector is linearized or fragmented using a restriction enzyme that cuts within the MCS to enable exogenous sequences to be ligated to the vector. “Ligation” refers to the process of forming phosphodiester bonds between two nucleic acid fragments, which may or may not be contiguous with each other. Techniques involving restriction enzymes and ligation reactions are well known to those of skill in the art of recombinant technology.

4. Termination Signals

The vectors or constructs of the present invention will generally comprise at least one termination signal. A “termination signal” or “terminator” is comprised of the DNA sequences involved in specific termination of an RNA transcript by an RNA polymerase. Thus, in certain embodiments a termination signal that ends the production of an RNA transcript is contemplated. A terminator may be necessary in vivo to achieve desirable message levels.

In eukaryotic systems, the terminator region may also comprise specific DNA sequences that permit site-specific cleavage of the new transcript to expose a polyadenylation site. This signals a specialized endogenous polymerase to add a stretch of about 200 A residues (polyA) to the 3′ end of the transcript. RNA molecules modified with this polyA tail appear to more stable and are translated more efficiently. Thus, in other embodiments involving eukaryotes, it is preferred that that terminator comprises a signal for the cleavage of the RNA, and it is more preferred that the terminator signal promotes polyadenylation of the message. The terminator and/or polyadenylation site elements can serve to enhance message levels and/or to minimize read through from the cassette into other sequences.

Terminators contemplated for use in the invention include any known terminator of transcription described herein or known to one of ordinary skill in the art, including but not limited to, for example, the termination sequences of genes, such as for example the bovine growth hormone terminator or viral termination sequences, such as for example the SV40 terminator. In certain embodiments, the termination signal may be a lack of transcribable or translatable sequence, such as due to a sequence truncation.

5. Polyadenylation Signals

For expression, particularly eukaryotic expression, one will typically include a polyadenylation signal to effect proper polyadenylation of the transcript. The nature of the polyadenylation signal is not believed to be crucial to the successful practice of the invention, and/or any such sequence may be employed. Preferred embodiments include the SV40 polyadenylation signal and/or the bovine growth hormone polyadenylation signal, convenient and/or known to function well in various target cells. Polyadenylation may increase the stability of the transcript or may facilitate cytoplasmic transport.

6. Origins of Replication

In order to propagate a vector in a host cell, it may contain one or more origins of replication sites (often termed “ori”), which is a specific nucleic acid sequence at which replication is initiated. Alternatively, an autonomously replicating sequence (ARS) can be employed if the host cell is yeast.

7. Selectable and Screenable Markers

In certain embodiments of the invention, the cells containing a nucleic acid construct of the present invention may be identified in vitro or in vivo by including a marker in the expression vector. Such markers would confer an identifiable change to the cell permitting easy identification of cells containing the expression vector. Generally, a selectable marker is one that confers a property that allows for selection. A positive selectable marker is one in which the presence of the marker allows for its selection, while a negative selectable marker is one in which its presence prevents its selection. An example of a positive selectable marker is a drug resistance marker.

Usually the inclusion of a drug selection marker aids in the cloning and identification of transformants, for example, genes that confer resistance to neomycin, puromycin, hygromycin, DHFR, GPT, zeocin and histidinol are useful selectable markers. In addition to markers conferring a phenotype that allows for the discrimination of transformants based on the implementation of conditions, other types of markers including screenable markers such as GFP, whose basis is calorimetric analysis, are also contemplated. Alternatively, screenable enzymes such as herpes simplex virus thymidine kinase (tk) or chloramphenicol acetyltransferase (CAT) may be utilized. One of skill in the art would also know how to employ immunologic markers, possibly in conjunction with FACS analysis. The marker used is not believed to be important, so long as it is capable of being expressed simultaneously with the nucleic acid encoding a gene product. Further examples of selectable and screenable markers are well known to one of skill in the art.

B. Host Cells

As used herein, the terms “cell,” “cell line,” and “cell culture” may be used interchangeably. All of these terms also include their progeny, which refers to any and all subsequent generations. It is understood that all progeny may not be identical due to deliberate or inadvertent mutations. In the context of expressing a heterologous nucleic acid sequence, “host cell” refers to a prokaryotic or eukaryotic cell, and it includes any transformable organisms that is capable of replicating a vector and/or expressing a heterologous gene encoded by a vector. A host cell can, and has been, used as a recipient for vectors. A host cell may be “transfected” or “transformed,” which refers to a process by which exogenous nucleic acid is transferred or introduced into the host cell. A transformed cell includes the primary subject cell and its progeny.

Host cells may be derived from prokaryotes or eukaryotes, depending upon whether the desired result is replication of the vector, expression of part or all of the vector-encoded nucleic acid sequences, or production of infectious viral particles. Numerous cell lines and cultures are available for use as a host cell, and they can be obtained through the American Type Culture Collection (ATCC), which is an organization that serves as an archive for living cultures and genetic materials. An appropriate host can be determined by one of skill in the art based on the vector backbone and the desired result. A plasmid or cosmid, for example, can be introduced into a prokaryote host cell for replication of many vectors. Bacterial cells used as host cells for vector replication and/or expression include DH5α, JM109, and KC8, as well as a number of commercially available bacterial hosts such as SURE® Competent Cells and SOLOPACK™ Gold Cells (STRATAGENE®, La Jolla). Alternatively, bacterial cells such as E. coli LE392 could be used as host cells for phage viruses.

Examples of eukaryotic host cells for replication and/or expression of a vector include HeLa, NIH3T3, Jurkat, 293, Cos, CHO, Saos, and PC12. Many host cells from various cell types and organisms are available and would be known to one of skill in the art. Similarly, a viral vector may be used in conjunction with either an eukaryotic or prokaryotic host cell, particularly one that is permissive for replication or expression of the vector.

C. Expression Systems

Numerous expression systems exist that comprise at least all or part of the compositions discussed above. Prokaryote- and/or eukaryote-based systems can be employed for use with the present invention to produce nucleic acid sequences, or their cognate polypeptides, proteins and peptides. Many such systems are commercially and widely available.

The insect cell/baculovirus system can produce a high level of protein expression of a heterologous nucleic acid segment, such as described in U.S. Pat. Nos. 5,871,986 and 4,879,236, both herein incorporated by reference, and which can be bought, for example, under the name MAXBAC® 2.0 from INVITROGEN® and BACPACK® BACULOVIRUS EXPRESSION SYSTEM from CLONTECH®.

Other examples of expression systems include STRATAGENE®'S COMPLETE CONTROL® Inducible Mammalian Expression System, which involves a synthetic ecdysone-inducible receptor, or its pET Expression System, an E. coli expression system. Another example of an inducible expression system is available from INVITROGEN®, which carries the T-REX® (tetracycline-regulated expression) System, an inducible mammalian expression system that uses the full-length CMV promoter. The Tet-On™ and Tet-Off™ systems from CLONTECH® can be used to regulate expression in a mammalian host using tetracycline or its derivatives. The implementation of these systems is described in Gossen et al., 1992 and Gossen et al., 1995, and U.S. Pat. No. 5,650,298, all of which are incorporated by reference.

INVITROGEN® also provides a yeast expression system called the Pichia methanolica Expression System, which is designed for high-level production of recombinant proteins in the methylotrophic yeast Pichia methanolica. One of skill in the art would know how to express a vector, such as an expression construct, to produce a nucleic acid sequence or its cognate polypeptide, protein, or peptide.

D. Introduction of Nucleic Acids into Cells

In certain embodiments, a nucleic acid may be introduce into a cell in vitro for production of polypeptides or in vivo for immunization purposes. There are a number of ways in which nucleic acid molecules such as expression vectors may be introduced into cells. In certain embodiments of the invention, the expression vector comprises a Flavivirus infectious particle or engineered vector derived from a Flavivirus genome. In other embodiments, an expression vector known to one of skill in the art may be used to express a segment of a Flavivirus nucleic, which may be translated into a Flavivirus polypeptide or peptide. The ability of certain viruses to enter cells via receptor-mediated endocytosis, to integrate into host cell genome and express viral genes stably and efficiently have made them attractive candidates for the transfer of foreign genes into mammalian cells (Ridgeway, 1988; Nicolas and Rubenstein, 1988; Baichwal and Sugden, 1986; Temin, 1986).

“Viral expression vector” is meant to include those vectors containing sequences of that virus sufficient to (a) support packaging of the vector and (b) to express a polynucleotide that has been cloned therein. In this context, expression may require that the gene product be synthesized. A number of such viral vectors have already been thoroughly researched, including adenovirus, adeno-associated viruses, retroviruses, herpesviruses, and vaccinia viruses.

Delivery may be accomplished in vitro, as in laboratory procedures for transforming cells lines, or in vivo or ex vivo, as in the treatment of certain disease states. One mechanism for delivery is via viral infection where the expression vector is encapsidated in an infectious viral particle. Several non-viral methods for the transfer of expression vectors into cultured mammalian cells also are contemplated by the present invention. These include calcium phosphate precipitation (Graham and Van Der Eb, 1973; Chen and Okayama, 1987; Rippe et al., 1990) DEAE-dextran (Gopal, 1985), electroporation (Tur-Kaspa et al., 1986; Potter et al., 1984), direct microinjection (Harland and Weintraub, 1985), DNA-loaded liposomes (Nicolau and Sene, 1982; Fraley et al., 1979) and lipofectamine-DNA complexes, cell sonication (Fechheimer et al., 1987), gene bombardment using high velocity microprojectiles (Yang et al., 1990), liposome (Ghosh and Bachhawat, 1991; Kaneda et al., 1989) and receptor-mediated transfection (Wu and Wu, 1987; Wu and Wu, 1988). Some of these techniques may be successfully adapted for in vivo or ex vivo use.

In certain embodiments, the nucleic acid encoding a gene or genes may be stably integrated into the genome of the cell. This integration may be in the cognate location and orientation via homologous recombination (gene replacement) or it may be integrated in a random, non-specific location (gene augmentation). In yet further embodiments, the nucleic acid may be stably maintained in the cell as a separate, episomal segment of DNA. Such nucleic acid segments or “episomes” encode sequences sufficient to permit maintenance and replication independent of or in synchronization with the host cell cycle. How the expression vector is delivered to a cell and where in the cell the nucleic acid remains is dependent on the type of expression vector employed.

Transfer of a nucleic acid molecule may be performed by any of the methods mentioned above which physically or chemically permeabilize the cell membrane. This is particularly applicable for transfer in vitro, but it may be applied to in vivo use as well.

Anti-HIV Therapies

In certain embodiments, therapeutic methods will include administering to a patient or subject a composition comprising an antigen or an antibody derived from a Flavivirus NS5A peptide or polypeptide, such as human or humanized animal derived antibodies. In various embodiments, the treatment methods of the invention may be used in combination with other anti-HIV treatments, such as Flavivirus infection as a therapeutic or preventative treatment for AIDS. For exemplary compositions and methods see PCT application WO 01/77157, which is incorporated herein by reference.

As a therapeutic measure, a Flavivirus NS5A agent can be used to reduce the severity or progression of AIDS, including the prevention of AIDS in HIV-infected individuals. A reduction in severity or progression of AIDS includes, but is not limited to, prevention of or a reduction in the severity, duration, or discomfort associated with the following conditions: prolonged and unexplained fatigue; swollen glands; prolonged fever; chills; excessive sweating; swollen gums and mouth lesions; sore throat; cough; shortness of breath; constipation; diarrhea; symptoms of well-known opportunistic infections; Kaposi sarcomas; skin rashes or lesions; loss of appetite or weight loss; malaise; headaches; speech impairment; muscle atrophy; memory loss; reduced cognitive functioning; swelling of the joints; joint stiffness or pain; cold intolerance; pain or tenderness in bones; energy level; anxiety, stress, and tension; groin lump; pruritus; genital sores; blurred or decreased vision; diplopia; light sensitivity; pain in chest, sides, back, muscle or stomach; and seizures.

As a preventative measure, a patient may be administered a pharmaceutically acceptable composition comprising a Flavivirus NS5A peptide or polypeptide. This agent may be used in conjunction with infection of CD4+ T cells with Flavivirus or a recombinant version of Flavivirus to inhibit infection of these cells by HIV. Alternatively, treatment with the Flavivirus NS5A compositions of the present invention may effect a combination of preventative and therapeutic treatments insofar as infection of other cells in an HIV-infected subject's body is prevented or attenuated.

Inhibition of AIDS progression may be demonstrated by reduction of detectable HIV in the HIV-infected subject; maintaining a CD4 count above 200 for a longer than average period of time; maintaining a normal T cell count; or maintaining normal p24 antigen. The term “therapeutic benefit” or “therapeutic effect” used throughout this application refers to anything that promotes or enhances the well-being of the subject with respect to the medical treatment of his/her condition, which includes treatment of HIV-infection (before the onset of AIDS), AIDS, as well as treatment of Hepatitis C. A list of nonexhaustive examples of this includes extension of the subject's life by any period of time; decrease or delay in the progression of AIDS (HIV, as described above) or Hepatitis C; decrease in viral load of HIV or HCV; decrease in HIV replication; clearance of HIV or HCV viremia reduced transmission of HCV or HIV; decrease in liver damage or complications; and a decrease in pain to the subject that can be attributed to the subject's condition.

Combination Therapies

Of course it is understood that the method of the present invention, particularly administration of NS5A agents as treatment for an HIV-infected subject, may also be used in combination with the administration of traditional therapies. Alternatively, the compositions of the present invention may be given in combination with treatment or prevention of hepatitis C, such as a-interferon. Some such therapies are described below.

In many clinical situations, it is advisable to use a combination of distinct therapies. Thus, it is envisioned that, in addition to the therapies described herein, one would also wish to provide to the patient more “standard” pharmaceutical anti-retroviral therapies. Examples of standard therapies are provided below.

Combinations may be achieved by administering to a patient a single composition or pharmacological formulation that includes both agents, or by administering to a patient two distinct compositions or formulations, at the same time, wherein one composition may include a Flavivirus NS5A, or expression construct encoding such, and the other includes the standard anti-retroviral therapy. Alternatively, a Flavivirus-based therapeutic may precede or follow the other treatment by intervals ranging from minutes to weeks. In embodiments where the other agent and NS5A are adminstered separately to the patient, one would generally ensure that a significant period of time did not expire between the time of each delivery, such that the agent and NS5A would still be able to exert an advantageously combined effect on the patient. In such instances, it is contemplated that one would administer to the patient both modalities within about 12-24 hours of each other and, more preferably, within about 6-12 hours of each other, with a delay time of only about 12 hours being most preferred. In some situations, it may be desirable to extend the time period for treatment significantly, however, where several days (2, 3, 4, 5, 6, or 7) to several weeks (1, 2, 3, 4, 5, 6, 7, or 8) lapse between the respective administrations.

It also is conceivable that more than one administration of a NS5A-based therapeutic agent will be desired. Various combinations may be employed, where a NS5A is “A” and the other agent is “B,” as exemplified below: A/B/A B/A/B B/B/A A/A/B B/A/A A/B/B B/B/B/A B/B/A/B A/A/B/B A/B/A/B A/B/B/A B/B/A/A B/A/B/A B/A/A/B B/B/B/A A/A/A/B B/A/A/A A/B/A/A A/A/B/A A/B/B/B B/A/B/B B/B/A/B Other combinations are contemplated as well.

A. AZT

A well known, traditional therapy for the treatment of AIDS involves zovidovudine (AZT™ available from Burroughs Wellcome). This is one of a class of nucleoside analogues known as dideoxynucleosides which block HIV replication by inhibiting HIV reverse transcriptase. The anti-AIDS drug zidovudine (also known as AZT) may also be used in limited circumstances, mostly in combination with rifampin, as described by Burger et al. (1993).

The compositions and methods disclosed herein will be particularly effective in conjunction with other forms of therapy, such as AZT and/or protease inhibitors that are designed to inhibit viral replication, by maintaining desirable levels of white blood cells. This, in effect, buys the patient the time necessary for the anti-viral therapies to work.

B. HAART

New combination drug therapy has shown promising results in the treatment of HIV-infected patients. Treatment with potent anti-HIV drug combinations is referred to as “highly active anti-retroviral therapy” (HAART), and it has provided clinical improvement, longer survival, and improved quality of life for people infected with HIV during all four stages of HIV disease. Examples of HAART include a protease inhibitor (indinavir, nelfinavir, ritonavir, ritonavir/saquinavir, or saquinavir) combined with two nucleoside analogs (AZT/ddI, d4T/ddI, AZT/ddC, AZT/3TC, or d4T/3TC).

In many instances, it will be desirable to have multiple administrations of the inventive compositions and/or a vaccines, usually not exceeding six administrations or vaccinations, more usually not exceeding four vaccinations. In certain embodiments, one or more, usually at least about three administrations or vaccinations may be provided. The administrations or vaccinations will normally be at from two to twelve week intervals, more usually from three to five week intervals. Periodic boosters at intervals of 1-5 years, usually three years, will be desirable to maintain protective levels of the antibodies. The course of the immunization or treatment may be followed by standard antibody assays. The assays may be performed by labeling with conventional labels, such as radionuclides, enzymes, fluorescents, and the like. These techniques are well known and may be found in a wide variety of patents, such as U.S. Pat. Nos. 3,791,932; 4,174,384 and 3,949,064, as illustrative of these types of assays.

The manner of application may be varied widely. Any of the conventional methods for administration of an antibody or vaccine are applicable. These are believed to include oral application on a solid physiologically acceptable base or in a physiologically acceptable dispersion, parenterally, by injection or the like. The dosage of the NS5A agent will depend on the route of administration and will vary according to the size of the host.

The NS5A agents and flavivirus nucleic acids of the invention may be formulated into a pharmaceutically acceptable composition, see below, or vaccine as neutral or salt forms. Pharmaceutically-acceptable salts include the acid addition salts (formed with the free amino groups of the peptide) and those that are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups may also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, 2-ethylamino ethanol, histidine, procaine, and the like.

The preparation of flavivirus NS5A agents as active ingredients is generally well understood in the art by analogy, as exemplified by U.S. Pat. Nos. 6,479,243, 6,399,763, 5,714,153, 5,582,981, and 4,833,077, all incorporated herein by reference. The preparation of vaccines that contain flavivirus sequences as active ingredients is generally well understood in the art by analogy, as exemplified by U.S. Pat. Nos. 5,958,895, 6,004,799, and 5,620,896, all incorporated herein by reference.

Pharmaceutical Compositions and Routes of Administration

Pharmaceutical compositions including NS5A peptides and polypeptides will be formulated along the line of typical pharmaceutical drug and biological preparations. A discussion of formulations may be found in Remington's Pharmaceutical Sciences (1990). The percentage of active compound in any pharmaceutical preparation is dependent upon both the activity of the compound, in this case ability of NS5A agents to inhibit HIV replication. Typically, such compositions should contain at least 0.1% active compound. The percentage of the compositions and preparations may, of course, be varied and may conveniently be between about 2 to about 60% of the weight of the unit. The amount of active compounds in such therapeutically useful compositions is such that a suitable dosage will be obtained.

The pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions. In all cases, the form must be sterile and must be fluid to the extent that easy injection is possible. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and vegetable oils. The proper fluidity can be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. The prevention of the action of microorganisms can be brought about by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, phenylmecuric nitrate, m-cresol, and the like. In many cases, it will be preferable to use isotonic solutions, for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate, and gelatin.

Sterile injectable solutions are prepared by incorporating the active compounds in the required amount in the appropriate solvent with various of the other ingredients enumerated above, as required, followed by sterile filtration. Generally, dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum drying and freeze-drying techniques that yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.

The phrases “pharmaceutically acceptable” or “pharmacologically acceptable” refer to molecular entities and compositions that do not produce an adverse, allergic, or other untoward reaction when administered to an animal, or human, as appropriate. As used herein, “pharmaceutically acceptable carrier” includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like. The use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredients, its use in the therapeutic compositions is contemplated. Supplementary active ingredients, such as other anti-cancer agents, can also be incorporated into the compositions.

The active compounds of the present invention can be formulated for parenteral administration, e.g., formulated for injection via the intravenous, intramuscular, intrathoracic, sub-cutaneous, or even intraperitoneal routes. Administration by i.v. or i.m. are specifically contemplated. Pharmaceutically acceptable salts, include the acid salts and those which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups may also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, 2-ethylamino ethanol, histidine, procaine, and the like.

In certain embodiments, it may be desirable to provide a continuous supply of therapeutic compositions to the patient. For intravenous or intraarterial routes, this is accomplished by drip system. For various approaches, delayed release formulations could be used that provided limited but constant amounts of the therapeutic agent over and extended period of time. For internal application, continuous perfusion may be preferred. This could be accomplished by catheterization followed by continuous administration of the therapeutic agent. The time period for perfusion would be selected by the clinician for the particular patient and situation, but times could range from about 1-2 hours, to 2-6 hours, to about 6-10 hours, to about 10-24 hours, to about 1-2 days, to about 1-2 weeks or longer. Generally, the dose of the therapeutic composition via continuous perfusion will be equivalent to that given by single or multiple injections, adjusted for the period of time over which the injections are administered. It is believed that higher doses may be achieved via perfusion, however.

For parenteral administration in an aqueous solution, for example, the solution should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose. These particular aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous and intraperitoneal administration. In this connection, sterile aqueous media that can be employed will be known to those of skill in the art in light of the present disclosure. For example, one dosage could be dissolved in 1 mL of isotonic NaCl solution and either added to 1000 mL of hypodermoclysis fluid or injected at the proposed site of infusion, (see for example, Remington's Pharmaceutical Sciences, 1990). Some variation in dosage will necessarily occur depending on the condition of the subject being treated. The person responsible for administration will, in any event, determine the appropriate dose for the individual subject.

An effective amount of the therapeutic composition is determined based on the intended goal. The term “unit dose” or “dosage” refers to physically discrete units suitable for use in a subject, each unit containing a predetermined-quantity of the therapeutic composition calculated to produce the desired responses, discussed above, in association with its administration, i.e., the appropriate route and treatment regimen. The quantity to be administered, both according to number of treatments and unit dose, depends on the protection desired.

Peptides or polypeptides may be administered in a dose that can vary from 0.01, 0.05, 0.1, 0.5, 1, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100 mg/kg of weight to 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200 mg/kg of weight in one or more daily, weekly, monthly, or yearly administrations during one or various days, weeks, months, or years. The antibodies can be administered by parenteral injection (intravenous, intraperitoneal, intramuscular, subcutaneous, intracavity or transdermic). For viral vectors, one generally will prepare a viral vector stock. Depending on the kind of virus and the titer attainable, one will deliver 1 to 100, 10 to 50, 100-1000, or up to 1×10⁴, 1×10⁵, 10⁶, 1×10⁷, 1×10⁸, 1×10⁹, 1×10¹⁰, 1×10¹¹, or 1×10¹² infectious particles to the patient. Similar figures may be extrapolated for liposomal or other non-viral formulations by comparing relative uptake efficiencies. Formulation as a pharmaceutically acceptable composition is discussed below.

In many instances, it will be desirable to have multiple administrations of the NS5A agent. The compositions of the invention may be administered 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more times. The administrations will normally be at from one to twelve week intervals, more usually from one to four week intervals. Periodic re-administration will be desirable with recurrent exposure to the pathogen (e.g., HIV). For example, an HIV positive mother would be re-inoculated prior to parturition from a second pregnancy.

Precise amounts and delivery regimen for the therapeutic composition also depend on the judgment of the practitioner and are peculiar to each individual. Factors affecting dose include physical and clinical state of the patient, the route of administration, the intended goal of treatment (alleviation of symptoms versus cure) and the potency, stability, and toxicity of the particular therapeutic substance.

In a particular embodiment of the invention, the NS5A agent may be entrapped in a liposome. Liposomes are vesicular structures characterized by a phospholipid bilayer membrane and an inner aqueous medium. Multilamellar liposomes have multiple lipid layers separated by aqueous medium. They form spontaneously when phospholipids are suspended in an excess of aqueous solution. The lipid components undergo self-rearrangement before the formation of closed structures and entrap water and dissolved solutes between the lipid bilayers (Ghosh and Bachhawat, 1991).

Current in vivo lipid delivery methods use subcutaneous, intradermal, intratumoral, or intracranial injection to avoid the toxicity and stability problems associated with cationic lipids in the circulation. The DOTAP:cholesterol lipid formulation is said to form a unique structure termed a “sandwich liposome.” This formulation is reported to “sandwich” DNA between an invaginated bi-layer or ‘vase’ structure. Beneficial characteristics of these lipid structures include a positive ρ, colloidal stabilization by cholesterol, two dimensional DNA packing and increased serum stability.

The production of lipid formulations often is accomplished by sonication or serial extrusion of liposomal mixtures after (I) reverse phase evaporation (II) dehydration-rehydration (III) detergent dialysis and (IV) thin film hydration. Once manufactured, lipid structures can be used to encapsulate compounds that are toxic (chemotherapeutics) or labile (nucleic acids) when in circulation. Lipid encapsulation has resulted in a lower toxicity and a longer serum half-life for such compounds (Gabizon et al., 1990).

EXAMPLES

The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventors to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.

Example 1

Cells: Tet-Off Jurkat cells (Clontech) were transfected with pTRE 2 Hyg plasmids containing full-length GBV-C NS5A (from the full-length GBV-C infectious clone AF121950) or with the vector only (control) by electroporation. Transfectants were selected using hygromycin, and cell lines cloned twice. Cells were grown in RPMI 1640 with or without doxycycline as recommended.

NS5A expression: Cells were lysed in RIPA buffer containing protease and phosphatase inhibitors and examined by immunoblot using rabbit anti-NS5A antisera.

HIV infections: Clinical and laboratory CXCR4 tropic strains of HIV-1 were used to infect Jurkat cell lines expressing NS5A or the vector control. Cells were maintained in doxycycline at various concentrations to inhibit NS5A expression. HIV replication was measured using culture supernatant p24 antigen ELISA.

Results: Jurkat cell lines stably expressing GBV-C NS5A protein were established, and expression of NS5A was regulated by doxycycline. HIV infection of cells expressing NS5A was decreased, as measured by p24 antigen compared to control cells or NS5A-containing cells grown in the pesence of doxycycline. NS5A-expressing cells also had lower surface density of CXCR4 and released increased levels of the CXCR4 ligand SDF-1 into culture supernatants, which may account for observations. In addition, NS5A led to increased levels of two genes associated with resistance to apoptosis, and rendered cells resistant to Fas-mediated apoptosis. This latter observation may account for slower decline in CD4 cell counts observed in HIV-infected people.

Summary: Jurkat cell lines stably expressing GBV-C NS5A protein (regulated by doxycycline) were established (FIG. 1). HIV infection of Jurkat cells that expressed GBV-C NS5A resulted in decreased levels of HIV replication (measured by p24 antigen) compared to vector control cells or cells in which NS5A expression was reduced by growth in doxycycline (FIGS. 2A-C). NS5A expressing cells had lower levels of CXCR4 on the surface than vector control cells, and also had reduced release of SDF-1 into culture supernatants, suggesting that NS5A expression may interact with chemokine receptor pathways (FIGS. 3A-B). Although part of the HIV inhibitory effect of GBV-C is mediated by E2 protein interactions with cellular receptor(s), the NS5A protein appears to also contribute to an anti-HIV effect of GBV-C (FIGS. 4A-B). GBV-C NS5A, like HCV, appears to have two phosphorylation states. HCV NS5A hyperphosphorylation has been reported by some to require NS4 expression. These data show that NS4 is not required for hyperphosphorylation of GBV-C NS5A (FIG. 5). NS5A led to relative resistance to Fas-mediated apoptosis, which could slow CD4 cell decline. HCV NS5A has previously been shown to be anti-apoptotic (FIG. 6). GBV-C infected PBMCs did not show decreased CXCR4 expression, although CCR5 expression was reduced. Because active GBV-C replication is required to produce NS5A, and active replication occurs in a small percentage of PBMCs, downregulation of CXCR4 would be missed. In contrast, E2 (structural protein) is released into supernatant and will have more widespread effects leading to decreased CCR5 (FIG. 7).

Example 2 NS5A Inhibition of HIV Replication is Dose Dependent, Independent of PKR and May Involve SDF-1

Using Jurkat cells that are infected with HIV, doxycycline-repessable expression constructs encoding GBV-C NS5A were used to inhibit HIV replication. As shown in FIG. 8, the use of 0, 0.01, 0.1 and 1 jig of doxycycline produced decreasing amounts of HIV inhibition as measured by p24 antigen levels. No such effect was seen in control Jurkat cells.

The inventors previously showed that NS5A's from interferon resistant (IFN-R) GBV-C inhibited PKR-mediated phosphorylation of eIF2α, which is part of the inteferon cascade, whereas interferon sensitive (IFN-S) did not. The NS5A's from IFN-R and IFN-S strains were compared for their respective abilities to inhibit HIV replication. As shown in FIG. 9, both strains were equally effective at inhibiting HIV replication as measured by p24 antigen concentration. Thus, the effect is apparently not related to PKR-function.

Following treatment with of HIV-infected Jurkat cells with NS5A, SDF-1 is released into culture supernatants (data not shown). In an effort to determine whether there is any link between SDF-1 and HIV inhibition, anti-SDF-1 antibodies were added to the Jurkat cell cultures. As shown in FIG. 10, there was an increase in HIV replication ranging from 50% to almost 60% as compared to unreated controls, thereby suggesting that SDF-1 might play a role.

Example 3 NS5A Inhibits Distinct Strains of HIV

Three different strains of HIV—ELI (X4) Clade D, JF (X4) Clade B and MN (X4) Clade B—were tested for replication in the presence of NS5A. As shown in FIGS. 11A-C, all were sensitive to NS5A-mediated inhibition.

Example 4 GBV-C NS5A Fragments Inhibit HIV Replication

A variety of NS5A fragments were tested for their ability to inhibit HIV replication.

Methods. Stable Jurkat cell lines expressing PKR-inhibiting and non-inhibiting NS5A proteins were generated, as were a series of C-terminal deletion mutants (FIG. 12). These cell lines expressed NS5A proteins of 123, 161, 181, 250, 314, and 363 amino acids (aa). All constructs had stop codons after NS5A, followed by the EMC IRES and GFP. A control cell line expressing only GFP served as a negative control, and NS5A and GFP expression were regulated by tetracycline. HIV replication was measured by p24 antigen release into culture supernatant or by measuring infectivity.

Results. Jurkat cell lines demonstrated regulated expression of NS5A and deletion mutants as shown by western blot and GPF expression. The NS5A and GFP genes were shown to remain linked by RT-PCR of cellular DNA from recombinant cell lines. Expression of either PKR-inhibiting or non-inhibiting NS5A proteins resulted in HIV inhibition (>95% reduction in p24 antigen), thus the HIV- and PKR-inhibiting functions are independent. All deletion mutants of 250 aa or larger retained HIV-inhibiting effects, whereas those with 181 aa or smaller did not (FIG. 13).

Example 5 HCV and GBV-B Virus NS5A Proteins Inhibit HIV Replication in Jurkat Cells

Hepatitis C virus (HCV), like GBV-C, commonly infect humans. GBV-B is a primate virus that is closely related to both HCV and GBV-C. HCV and GBV-C NS5A proteins both inhibit PKR function. To further. characterize the inventors work showing inhibition of X4-tropic HIV replication, they expressed HCV and GBV-B NS5A's and a series of GBV-C NS5A deletions in Jurkat cells, and measured the effect of these proteins on HIV replication.

Methods. Jurkat cell lines stably expressing HCV, GBV-B, and GBV-C NS5A proteins were generated, as were a series of GBV-C NS5A deletion mutants. All constructs had stop codons after NS5A, followed by the EMC IRES and GFP. A control cell line expressing only GFP served as a negative control, and NS5A and GFP expression were regulated by tetracycline. Plasmids were transfected using the Amaxa nucleofection method, cells were selected for growth in hygromycin and for GFP expression. HIV replication was measured by p24 antigen release into culture supernatant or by measuring infectivity.

Results. Jurkat cell lines demonstrated regulated expression of HCV, GBV-B GBV-C NS5A proteins and GBV-C deletion mutants as determined by GFP expression and when antibodies were available, by immunoblot (FIG. 14). For constructs in which antibodies were not available, the NS5A and GFP coding sequences were linked (detected by PCR of cellular DNA). Expression of HCV, GBV-B and GBV-C NS5A proteins resulted in HIV inhibition (>95% reduction in p24 antigen), thus the inhibitory effect appears conserved between these three flaviviruses (FIG. 15). All deletion mutants containing GBV-C NS5A amino acids (aa) between number 152 and 237 retained HIV-inhibiting effects, whereas those with C-terminal deletions containing ≦152 NS5A aa's did not inhibit HIV replication (FIG. 16). The effect was reduced in NS5A containing cells grown in doxycycline (NS5A expression turned off), but not in control cells grown in doxycycline. Thus, expression of GBV-C, GBV-B, and HCV NS5A proteins resulted in inhibition of CXCR4-tropic HIV replication in Jurkat cells, and the inhibitory effect requires GBV-C aa's 152-237, coinciding with domain II of the HCV NS5A protein. The region may possibly narrowed to 152-182 (FIG. 17).

All of the compositions and methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. More specifically, it will be apparent that certain agents that are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.

REFERENCES

The following references, to the extent that they provide exemplary procedural or other details supplementary to those set forth herein, are specifically incorporated herein by reference.

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1. A pharmaceutical composition comprising an isolated flavivirus NS5A peptide or polypeptide.
 2. The composition of claim 1, comprising a flavivirus NS5A peptide.
 3. The composition of claim 2, comprising multiple flavivirus NS5A peptides.
 4. The composition of claim 1, comprising a flavivirus NS5A polypeptide.
 5. The composition of claim 4, wherein the flavivirus NS5A polypeptide is a full length NS5A polypeptide.
 6. The composition of claim 4, wherein the flavivirus NS5A polypeptide is a fusion polypeptide.
 7. The composition of claim 1, wherein the flavivirus NS5A peptide or polypeptide further comprises a targeting signal.
 8. The composition of claim 7, wherein the targeting signal is a nuclear targeting signal.
 9. The composition of claim 7, wherein the targeting signal targets a cell surface receptor.
 10. The composition of claim 9, wherein the cell surface receptor is the CD4 receptor.
 11. The composition of claim 1, wherein the flavivirus NS5A peptide or polypeptide is formulated in a lipid vehicle.
 12. The composition of claim 11, wherein the lipid vehicle is a liposome.
 13. The composition of claim 1, wherein said flavivirus NS5A peptide or polypeptide is formulated with an amphipathic peptide, an insect peptide, or pyrrhocoricin.
 14. The composition of claim 1, wherein the flavivirus is selected from the group consisting of DEN4, YFV, TBEV, WNV, CSFV, BVDV, GBV-A, GBV-B, GBV-C, HGV, HCV2a, HCV3a, HCV2b, HCV1a and HCV1b.
 15. The composition of claim 14, wherein the flavivirus is a GBV-C virus.
 16. The composition of claim 3, wherein the multiple peptides are from the same NS5A polypeptide.
 17. The composition of claim 3, wherein the multiple peptides are from different NS5A polypeptides.
 18. The composition of claim 1, wherein the flavivirus NS5A peptide or polypeptide comprises residues 152-237 of GBV-C NS5A, or the corresponding sequences thereto from other flavivirus NS5A proteins.
 19. The composition of claim 1, wherein the flavivirus NS5A peptide or polypeptide comprises domain II of HCV NS5A, or the corresponding sequences thereto from other flavivirus NS5A proteins.
 20. The composition of claim 1, wherein the flavivirus NS5A peptide or polypeptide is from a IFN-sensitive flavivirus.
 21. The composition of claim 1, wherein the flavivirus NS5A peptide or polypeptide is from a IFN-resistant flavivirus.
 22. The composition of claim 20, wherein the IFN-sensitive flavivirus is a GBV-C virus.
 23. The composition of claim 21, wherein the IFN-resistant flavivirus is a GBV-C virus.
 24. A method for preventing or treating HIV infection comprising administering to a subject a composition comprising a flavivirus NS5A peptide or polypeptide. 25.-46. (canceled)
 47. The method of claim 24, further comprising administration of at least a second anti-HIV therapy.
 48. The method of claim 47, wherein the second anti-HIV therapy is administered before said flavivirus NS5A peptide or polypeptide.
 49. The method of claim 48, wherein the second anti-HIV therapy is administered after said flavivirus NS5A peptide or polypeptide.
 50. The method of claim 47, wherein the second anti-HIV therapy is HAART therapy.
 51. The method of claim 47, wherein the second anti-HIV therapy is AZT therapy.
 52. The method of claim 24, wherein the composition is administered at least twice.
 53. A method of reducing HIV replication in an HIV-infected cell comprising contacting said cell with a composition comprising a flavivirus NS5A peptide or polypeptide.
 54. The method of claim 53, wherein the cell is a T lymphocyte.
 55. A method of inhibiting HIV infection of a cell comprising contacting said cell with a composition comprising a flavivirus NS5A peptide or polypeptide.
 56. The method of claim 55, wherein the cell is a T lymphocyte.
 57. A method for preventing or treating HIV infection comprising administering to a subject a composition comprising an expression construct encoding a flavivirus NS5A peptide or polypeptide. 58.-72. (canceled) 